Analysis of the algorithm: From rankings to backup genes.

Ranking section

Table 1. Performance summary for every kernel and net before integration.

Net Kernel tpr_down_ci_0.95 tpr_up_ci_0.95 fpr_down_ci_0.95 fpr_up_ci_0.95 f
biological_process ct 1 1 1 1 0.904761904761905
biological_process el 1 1 1 1 0.904761904761905
biological_process ka 1 1 1 1 0.904761904761905
biological_process rf 1 1 1 1 0.904761904761905
cellular_component ct 1 1 1 1 0.90625
cellular_component el 1 1 1 1 0.90625
cellular_component ka 1 1 1 1 0.90625
cellular_component rf 1 1 1 1 0.90625
disease ct 0.5 1 0 1 0.956521739130435
disease el 1 1 0.666666666666667 1 0.936170212765957
disease ka 1 1 0.333333333333333 1 0.936170212765957
disease rf 1 1 1 1 0.936170212765957
gene_TF el 1 1 0 0 1
gene_TF ka 1 1 1 1 0.5
gene_TF rf 1 1 0 0 1
gene_hgncGroup el 1 1 1 1 0.9
gene_hgncGroup ka 1 1 1 1 0.9
gene_hgncGroup rf 1 1 1 1 0.9
genetic_interaction_effect_bicor ct 1 1 1 1 0.896551724137931
genetic_interaction_effect_bicor el 1 1 1 1 0.896551724137931
genetic_interaction_effect_bicor ka 1 1 1 1 0.896551724137931
genetic_interaction_effect_bicor rf 1 1 1 1 0.896551724137931
molecular_function ct 1 1 1 1 0.90625
molecular_function el 1 1 1 1 0.90625
molecular_function ka 1 1 1 1 0.90625
molecular_function rf 0.620689655172414 1 0.5 1 0.919354838709677
pathway el 1 1 0.5 1 0.91304347826087
pathway ka 1 1 1 1 0.91304347826087
pathway rf 0.0952380952380952 1 0.25 1 0.933333333333333
phenotype ct 0.826086956521739 1 0.333333333333333 1 0.901960784313726
phenotype el 0.347826086956522 1 0 0.666666666666667 0.958333333333333
phenotype ka 1 1 0.5 1 0.884615384615384
phenotype rf 0.65108695652174 1 0 0.666666666666667 0.958333333333333
protein_interaction el 1 1 0.75 1 0.909090909090909
protein_interaction ka 1 1 1 1 0.909090909090909
protein_interaction rf 0.882916666666667 1 0.666666666666667 1 0.916030534351145

Table 2. Performance summary for every kernel after integration

Integration Kernel tpr_down_ci_0.95 tpr_up_ci_0.95 fpr_down_ci_0.95 fpr_up_ci_0.95 f
integration_mean_by_presence ct 0.413362068965518 1 0.583333333333333 1 0.910569105691057
integration_mean_by_presence el 1 1 0.75 1 0.909090909090909
integration_mean_by_presence ka 1 1 1 1 0.909090909090909
integration_mean_by_presence rf 1 1 0.75 1 0.909090909090909
mean ct 0.379310344827586 1 0.583333333333333 1 0.910569105691057
mean el 1 1 1 1 0.909090909090909
mean ka 1 1 1 1 0.909090909090909
mean rf 1 1 1 1 0.909090909090909

Backup Pairs Coverage By Layer Non integrated

Backup Pairs Coverage By Layer Integrated

Distribution of ranks in dataset by non integrated kernels

Distribution of ranks in dataset by Integrated kernels

ROC-AUCs for Non-integrated kernel and layer

ROC-AUCS for integrated kernels

CDF plots of non integrated kernels

ROC plots of non integrated kernels

ROC plots of integrated kernels

CDF plots of integrated kernels